From: List (zheng042003_at_yahoo.com)
Date: Mon Sep 29 2008 - 12:52:14 CDT
Dear NAMD experts,
I have a question around running MD for a CYCLOPEPTIDE. When the regular procedure was applied, after minization, the bond between the first and the last residues got broken. I guess these two residues are not connected in the .psf file although they are geometry-wise. I wonder if there is any way to specify the connectivity or apply any constraint, so that the first and last residues will remain bonded/connected throughout the MD simulation.
Any help will be greatly appreciated,
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:49:54 CST